Debug _cosmx_morphology_coords when one or more morphology channels are unused #233
Workflow file for this run
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: ci | |
| on: | |
| push: | |
| tags: | |
| - v* | |
| pull_request: | |
| branches: [main] | |
| jobs: | |
| pre-commit: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v3 | |
| - uses: pre-commit/action@v3.0.1 | |
| tests: | |
| needs: [pre-commit] | |
| name: "pytest and snakemake" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.10", "3.11", "3.12"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up the environment | |
| uses: ./.github/actions/setup-python-env | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install extra dependencies | |
| run: uv sync --extra cellpose --extra wsi --dev && uv run pip install snakemake 'pulp<2.8' | |
| - name: Tests | |
| run: uv run pytest | |
| - name: Snakemake | |
| run: cd workflow && uv run snakemake --config sdata_path=tuto.zarr --configfile=config/toy/cellpose.yaml --workflow-profile profile/ci -c1 | |
| deploy-docs: | |
| needs: [tests] | |
| if: contains(github.ref, 'tags') | |
| name: "Deploy documentation" | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up the environment | |
| uses: ./.github/actions/setup-python-env | |
| - name: Install extra dependencies | |
| run: uv sync --dev | |
| - name: Build documentation | |
| run: uv run mkdocs gh-deploy --force | |
| pypi-release: | |
| needs: [tests] | |
| if: contains(github.ref, 'tags') | |
| name: "PyPI release" | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up the environment | |
| uses: ./.github/actions/setup-python-env | |
| - name: Build | |
| run: uv build | |
| - name: Publish | |
| run: uv publish -t ${{ secrets.PYPI_TOKEN }} | |
| docker-images-release: | |
| needs: [pypi-release] | |
| if: contains(github.ref, 'tags') | |
| name: "Docker images release" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| extra-name: ["", "-baysor", "-cellpose", "-proseg", "-stardist"] | |
| steps: | |
| - name: Export tag version | |
| run: | | |
| TAG="${GITHUB_REF#refs/tags/v}" | |
| echo "VERSION=$TAG" >> $GITHUB_ENV | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Login to Docker Hub | |
| uses: docker/login-action@v3 | |
| with: | |
| username: ${{ vars.DOCKERHUB_USERNAME }} | |
| password: ${{ secrets.DOCKERHUB_TOKEN }} | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Build and push | |
| uses: docker/build-push-action@v6 | |
| with: | |
| push: true | |
| platforms: linux/amd64 | |
| tags: ${{ vars.DOCKERHUB_USERNAME }}/sopa:${{ env.VERSION }}${{ matrix.extra-name }} | |
| context: ./docker/sopa${{ matrix.extra-name }} | |
| build-args: | | |
| SOPA_VERSION=${{ env.VERSION }} |